[1] "libdir: /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/ClinicalAnalysisAllGenes_new/broadinstitute.org/cancer.genome.analysis/00333/60/"
[1] "terrence_modification_tag: TRUE"
[1] "op: "
[1] "dfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_RPPA_preprocess/LUAD-TP/11489610/LUAD-TP.rppa.txt"
[1] "cfn: /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LUAD-TP/11541582/LUAD-TP.merged_data.txt"
[1] "gv: ALL"
[1] "gfn: "
[1] "sfn: "
[1] "fv: ALL"
[1] "ofn: "
[1] "dx: "
[1] "cfn"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LUAD-TP/11541582/LUAD-TP.merged_data.txt"
[1] "ok3"

nSamples in clinical file=483, in expression file=181, common to both=181
Number of genes in original expression dataset=160
[1] "ALL"
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "KARNOFSKYPERFORMANCESCORE"             
[16] "HISTOLOGICALTYPE"                      
[17] "RADIATIONS.RADIATION.REGIMENINDICATION"
[18] "NUMBERPACKYEARSSMOKED"                 
[19] "YEAROFTOBACCOSMOKINGONSET"             
[20] "COMPLETENESS.OF.RESECTION"             
[21] "RACE"                                  
[22] "ETHNICITY"                             
[23] "BATCHNUMBER"                           

Input Data has 23 rows and 181 columns.

[1] "Batch" "23"   
[1] "Last Follow UP"
TCGA-05-4249 TCGA-05-4384 TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4405 
        1523          426           NA         1431           NA          610 
TCGA-05-4410 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4426 
          NA          455           NA          912          365          791 
TCGA-05-4430 TCGA-05-5420 TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
         761          457          151           30           62           14 
TCGA-38-4626 TCGA-38-4627 TCGA-38-6178 TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
        3674         1147          448         1429          400          741 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 TCGA-44-6145 
        1301         1130          190          722          383          328 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
         302          845          658          705         1938           NA 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7662 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
          NA          444          218          882          535          719 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
        2318           NA           NA         1081         1421          428 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
         999          268          896          157         1700          445 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5049 
         890          522          354           NA           NA         2146 
TCGA-50-5051 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
         455         1499          246          267         1091         2370 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6593 
          NA           NA          567          883          764           NA 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-53-7626 TCGA-53-7813 
          NA         1015           NA          255           NA          424 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-6543 TCGA-55-6712 TCGA-55-6970 
         701         1178         1375            2           24           NA 
TCGA-55-6971 TCGA-55-6978 TCGA-55-6979 TCGA-55-6981 TCGA-55-6982 TCGA-55-7573 
          25           NA           NA           NA           NA            4 
TCGA-55-7574 TCGA-55-7728 TCGA-55-7815 TCGA-55-7911 TCGA-64-1676 TCGA-64-1677 
          95           24           54           21         1728          628 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 
        1189         1686         1126           NA         2676         1305 
TCGA-64-5781 TCGA-67-3771 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
        1559          610          174          141          422          202 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-71-6725 TCGA-73-4658 
         186          690          414          165           61         1600 
TCGA-73-4659 TCGA-73-4675 TCGA-73-4676 TCGA-73-7498 TCGA-73-7499 TCGA-75-5122 
         711           40          164          621          519           NA 
TCGA-75-6203 TCGA-75-6205 TCGA-75-6207 TCGA-75-6211 TCGA-75-6212 TCGA-75-6214 
          NA           NA           NA           NA           NA           NA 
TCGA-75-7027 TCGA-75-7030 TCGA-75-7031 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 
          NA           NA           NA           NA           NA           NA 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
          NA         1093           NA         1202          760           NA 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
          NA           NA           NA         1221          678          215 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 
          NA         6812           NA           NA           NA           NA 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-80-5607 
          NA          327          881           NA          994           NA 
TCGA-80-5608 TCGA-86-6562 TCGA-86-6851 TCGA-86-7713 TCGA-91-6828 TCGA-91-6829 
          NA           NA           NA          422          323           NA 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-93-7348 
          79          372          842           35          492          127 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 TCGA-97-7546 
          34            2          568          477          476          964 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
        1932         1332          775          181           NA           22 
TCGA-99-7458 
         392 
Variable 1:'AGE':	nDistinctValues=43,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=60,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=123,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBERPACKYEARSSMOKED':	nDistinctValues=56,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 23:'BATCH.NUMBER':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "NEOPLASM.DISEASESTAGE"                 
 [3] "PATHOLOGY.T.STAGE"                     
 [4] "PATHOLOGY.N.STAGE"                     
 [5] "PATHOLOGY.M.STAGE"                     
 [6] "GENDER"                                
 [7] "KARNOFSKY.PERFORMANCE.SCORE"           
 [8] "HISTOLOGICAL.TYPE"                     
 [9] "RADIATIONS.RADIATION.REGIMENINDICATION"
[10] "NUMBERPACKYEARSSMOKED"                 
[11] "COMPLETENESS.OF.RESECTION"             
[12] "RACE"                                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 181 columns, 1 survival variables, and 12 non-survival variables.
                              D                 
            "D" "Time to Death"          "Year" 
AGE, nv=43, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=8, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "PATHOLOGY.T.STAGE"
[1] "num to class table"
vv1
  1   2   3   4 
 47 108  13  12 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "PATHOLOGY.N.STAGE"
[1] "num to class table"
vv1
  0   1   2   3 
106  34  34   1 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=6, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=9, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=56, binary=FALSE, numeric=TRUE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
[1] "saved param, results, example.expr in analysis.result.Rdata "
